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PDBsum entry 2fp1
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References listed in PDB file
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Key reference
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Title
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1.6 a crystal structure of the secreted chorismate mutase from mycobacterium tuberculosis: novel fold topology revealed.
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Authors
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M.Okvist,
R.Dey,
S.Sasso,
E.Grahn,
P.Kast,
U.Krengel.
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Ref.
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J Mol Biol, 2006,
357,
1483-1499.
[DOI no: ]
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PubMed id
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Abstract
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The presence of exported chorismate mutases produced by certain organisms such
as Mycobacterium tuberculosis has been shown to correlate with their
pathogenicity. As such, these proteins comprise a new group of promising
selective drug targets. Here, we report the high-resolution crystal structure of
the secreted dimeric chorismate mutase from M. tuberculosis (*MtCM; encoded by
Rv1885c), which represents the first 3D-structure of a member of this chorismate
mutase family, termed the AroQ(gamma) subclass. Structures are presented both
for the unliganded enzyme and for a complex with a transition state analog. The
protomer fold resembles the structurally characterized (dimeric) Escherichia
coli chorismate mutase domain, but exhibits a new topology, with helix H4 of
*MtCM carrying the catalytic site residue missing in the shortened helix H1.
Furthermore, the structure of each *MtCM protomer is significantly more compact
and only harbors one active site pocket, which is formed entirely by one
polypeptide chain. Apart from the structural model, we present evidence as to
how the substrate may enter the active site.
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Figure 4.
Figure 4. Proposed AroQ subclasses. The upper panels show
cylinder representations of the folds of (a) EcCM (PDB entry
1ECM; representative of the AroQ[a] subclass), (b) the ScCM
protomer (PDB entry 4CSM; representative of the AroQ[b]
subclass), and (c) the *MtCM protomer (PDB entry 2FP2;
representative of the AroQ[g] subclass). Termini and prominent
helices are labeled. The lower panels show the superimpositions
(ribbon representations) of (d) *MtCM (yellow) and EcCM
(red/blue; two protomers), (e) *MtCM (yellow) and ScCM (green),
and (f) *MtCM (yellow) and EcCM (blue; second protomer).
Superimpositions are with respect to the *MtCM structure. The
disulfide bond in *MtCM is highlighted by colored spheres. Note
that the active site is composed primarily of helices from the
N-terminal half in *MtCM, but from the C-terminal half in ScCM.
All structures are complexes with the transition state analog
inhibitor 1 (shown as stick model).
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Figure 6.
Figure 6. Active sites of *MtCM (a) and (d), EcCM (b) and
ScCM (c). In the schematic representation (a) of the *MtCM
active site, *MtCM residue labels are boxed and accompanied by
colored labels identifying the corresponding amino acid residues
of EcCM (blue/red; upper labels) and ScCM (green; lower labels).
The homolog of Arg72 in ScCM, Val197 (see Figure 3(a)), forms
part of a wall of the active site pocket, but does not seem to
interact directly with 1 and was therefore omitted. Residues
denoted with an asterisk are functional analogs but not sequence
homologs of Glu106. The transition state analog inhibitor 1 is
highlighted with heavy lines in (a), with yellow carbon atoms in
(b) and (c), and with orange carbon atoms in (d). Hydrogen bonds
are indicated by dotted lines. Note that in *MtCM, the
carboxylate oxygen O2 from inhibitor 1 has three possible
hydrogen bonding partners (with equally favorable geometries):
Arg49, Gln76 and a structural water molecule. This water
molecule, which simultaneously binds to the two carboxylate
groups of inhibitor 1, is tightly coordinated by Arg72 of *MtCM
and Arg51 of EcCM (residue shown only in Figure 6 and Figure 7,
due to crowding in the other pictures; the arginine side-chains
align in an antiparallel fashion with Arg134 and Arg11' of *MtCM
and EcCM, respectively). For *MtCM, the electron density is
shown in stereo representation (s[A]-weighted 2F[o] -F[c] map,
at 1s) (d). (e) and (f) give stereo views of superimpositions of
the three active sites from *MtCM (yellow carbon atoms), EcCM
(red/blue, for the two protomers) and ScCM (green). The view in
(f) is flipped along the horizontal axis of the paper plane,
with respect to the view in (e). Note the differential
positioning (leading to a swap of function) of the residues
corresponding to Val73/Glu106 of *MtCM (Glu52/Val85 in EcCM and
Glu198/Lys243 in ScCM, respectively), which are behind inhibitor
1 in (e) and above the plane in (f).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
357,
1483-1499)
copyright 2006.
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